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FGAP specifications

Information


Unique identifier OMICS_12016
Name FGAP
Interface Web user interface
Restrictions to use None
Input data FGAP uses a draft of the assembly and a set of contigs that are mapped against genome draft to close gaps using BLAST algorithms.
Output data The algorithm runs in multiple rounds, necessary to prevent overlapping between gaps close to each other. This prevents modifications in the query sequence of the neighbor gap. The output consists of one Fasta and one log file per round, and a final statistics file. The log file contains the alignment information for both sides of each gap. The Fasta file contains the new sequence with the gap sequence reported in the log file. Changes are incremental in the output Fasta files.
Computer skills Basic
Version 1.8.1
Stability No
Maintained No

Maintainer


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Information


Unique identifier OMICS_12016
Name FGAP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages MATLAB
License MIT License
Computer skills Advanced
Version 1.8.1
Stability No
Requirements
BLAST+, MCR
Source code URL http://www.bioinfo.ufpr.br/fgap/?p=download
Maintained No

Versioning


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Maintainer


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Publication for FGAP

FGAP citations

 (10)
library_books

Whole genome sequencing of Leptospira interrogans from southern Brazil: genetic features of a highly virulent strain

2018
PMCID: 5722262
PMID: 29236923
DOI: 10.1590/0074-02760170130

[…] against the genome of L. interrogans strain Fiocruz L1-130 (GenBank: AE016823.1, AE016824.1) and ordered using CAR () based on this same reference genome. Assembly gaps were closed using GMCloser (), FGAP (), and manual curation with the CLC Genome Workbench (http://www.clcbio.com). Genome annotation was performed using Genix () and manually reviewed using Artemis (). In silico multilocus sequence […]

library_books

Comparative Genomics of Sibling Species of Fonsecaea Associated with Human Chromoblastomycosis

2017
Front Microbiol
PMCID: 5640708
PMID: 29062304
DOI: 10.3389/fmicb.2017.01924

[…] was performed with FastQC and reads with quality below PHRED20 were removed (Andrews, ). The reads were assembled de novo using SPAdes v3.6.2 (Bankevich et al., ). The gap closure was performed with FGAP (Piro et al., ) and scaffolding with SSPACE (Boetzer et al., ). The mitochondrial genomes were assembled in Fonsecaea species by extracting reads using the complete mtDNA of Exophiala dermatitidi […]

library_books

Genome Sequence of Type Strain Fonsecaea multimorphosa CBS 980.96T, a Causal Agent of Feline Cerebral Phaeohyphomycosis

2017
Genome Announc
PMCID: 5313630
PMID: 28209838
DOI: 10.1128/genomeA.01666-16

[…] the paired-end (2 × 250 bp) sequencing method. A quality check of the sequenced reads was done using FastQC (). SPAdes version 3.6.2 () was used for de novo assembly. Gap closure was performed using FGAP () and assembly coverage was determined using Bowtie2 (). Gene prediction was performed using GeneMarkES version 4.29 (). Annotation of the protein coding genes was based on best-hit searches aga […]

library_books

Approaches for in silico finishing of microbial genome sequences

2017
Genet Mol Biol
PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] t (https://sourceforge.net/projects/jcontigsort/), which applies a HashMap-based algorithm using the k-mers from the draft genome and from a reference. Gaps between the contigs are then closed using jFGAP, a Java-implementation of the FGAP algorithm (), by taking information form alternative assemblies of the target genome. To identify misassembled regions, GFinisher uses an adaptation of the GC-s […]

library_books

GFinisher: a new strategy to refine and finish bacterial genome assemblies

2016
Sci Rep
PMCID: 5056350
PMID: 27721396
DOI: 10.1038/srep34963

[…] The FGap originally written in Matlab was rewritten in Java, preserving the same concept, and improved for working with contigs. This application is part of the GFinisher as jFGap. […]

library_books

Draft Genome Sequence of Fonsecaea nubica Strain CBS 269.64, Causative Agent of Human Chromoblastomycosis

2016
Genome Announc
PMCID: 4974309
PMID: 27491988
DOI: 10.1128/genomeA.00735-16

[…] 3.6.2 (). The draft genome comprised 258 contigs and the genome size was 33.7 Mb, with a G+C content of 52.46%. Protein-coding genes were predicted with GeneMark-ES (). Gap closure was performed with FGAP software (). Annotation for 11,681 predicted genes were assigned based on similarity searches against the nr database using RAFTS3 () and InterProScan () comparisons. The genome contained 36 tRNA […]

Citations

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FGAP institution(s)
Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, PR, Brazil
FGAP funding source(s)
National Institute of Science and Technologies of Biological Nitrogen Fixation, Fundação Araucária, CAPES, CNPq

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